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- PDB-7lx8: T4 lysozyme mutant L99A -

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Basic information

Entry
Database: PDB / ID: 7lx8
TitleT4 lysozyme mutant L99A
ComponentsLysozyme
KeywordsPROTEIN BINDING / mutant / lysozyme / small molecule / L99A / complex
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
1-chloro-2-(methylsulfanyl)benzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.03 Å
AuthorsKamenik, A.S. / Singh, I. / Lak, P. / Balius, T.E. / Liedl, K.R. / Shoichet, B.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Energy penalties enhance flexible receptor docking in a model cavity.
Authors: Kamenik, A.S. / Singh, I. / Lak, P. / Balius, T.E. / Liedl, K.R. / Shoichet, B.K.
History
DepositionMar 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9723
Polymers19,6921
Non-polymers2812
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.289, 60.289, 96.328
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lysozyme / Lysis protein / Endolysin / Muramidase


Mass: 19691.541 Da / Num. of mol.: 1 / Mutation: L99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-YGV / 1-chloro-2-(methylsulfanyl)benzene


Mass: 158.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7ClS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Isopropanol, PEG 4000, Tris-Cl pH 8.0, Beta-mercaptoethanol, 2-hyrdoxyethyl disulfide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.03→48.16 Å / Num. obs: 99343 / % possible obs: 98.8 % / Redundancy: 17.4 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.011 / Rrim(I) all: 0.049 / Net I/σ(I): 21.5 / Num. measured all: 1733212 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.03-1.057.92.6343314541850.3550.9742.8170.786.7
5.64-48.1618.50.0281331572110.0060.02874.799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W57

4w57


Resolution: 1.03→45.903 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 5034 5.07 %
Rwork0.2063 94205 -
obs0.2066 99239 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 38.36 Å2 / Biso mean: 17.1019 Å2 / Biso min: 10.54 Å2
Refinement stepCycle: final / Resolution: 1.03→45.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 17 116 1407
Biso mean--18.7 24.11 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041333
X-RAY DIFFRACTIONf_angle_d0.7561796
X-RAY DIFFRACTIONf_chiral_restr0.062196
X-RAY DIFFRACTIONf_plane_restr0.004230
X-RAY DIFFRACTIONf_dihedral_angle_d2.57805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.03-1.04170.37411500.3698262984
1.0417-1.0540.35871420.3526278289
1.054-1.06680.29481530.3262290193
1.0668-1.08030.3061830.2984304397
1.0803-1.09460.27591820.2819311599
1.0946-1.10950.25481550.26023141100
1.1095-1.12540.24282030.24663102100
1.1254-1.14220.22711850.22963166100
1.1422-1.160.22451760.22333160100
1.16-1.17910.2481880.2213096100
1.1791-1.19940.2341760.21313140100
1.1994-1.22120.211580.21313147100
1.2212-1.24470.20371670.21343205100
1.2447-1.27010.22111760.2093123100
1.2701-1.29770.19361730.20243142100
1.2977-1.32790.18961690.20713187100
1.3279-1.36110.23681810.20353152100
1.3611-1.39790.18511590.20513193100
1.3979-1.43910.19881590.20483177100
1.4391-1.48550.2181610.20173164100
1.4855-1.53860.20241610.19213200100
1.5386-1.60020.19721650.19223199100
1.6002-1.67310.21071780.19623185100
1.6731-1.76130.20061740.19923169100
1.7613-1.87160.22771730.1963211100
1.8716-2.01610.18861240.20323264100
2.0161-2.2190.22931360.19633269100
2.219-2.54010.20951710.2033233100
2.5401-3.20010.2491810.21513277100
3.2001-45.9030.17941750.19833433100

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